[Insight-users] Re: Segmentation on RAW Files: Watershed Module from Georgetown University

Luis Ibanez luis.ibanez@kitware.com
Thu, 27 Mar 2003 21:37:12 -0500


This is a multi-part message in MIME format.
--------------090605030207070506070903
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit


Hi Neha,

This may be your lucky day   :-)

As part of a project developed by the ISIS
center at Georgetown University,
http://www.isis.georgetown.edu/

a series of segmentation applications are being
developed. These small applications are built as
modules using ITK components.

Please find  attached the module intended to
perform Watershed segmentation in 3D.

You will find a module class that gets built into
a library, as well as an utility class that
produces a program to be invoked at the command
line.

This application will read any 3D image file format
supported by ITK. You can directly feed it now with
metaimages (as long as they contain 3D images).


---

The full library will contain about 9 segmentation
methods, all based in ITK components, and will be in
the public domain when it becomes stable.



Regards,


    Luis


----------------
Neha D wrote:
> Hi Luis,
> 
> Now, I am using MetaImageReaders to work with RAW images ( I have no 
> other alternative than using RAW format, since I need to operate on raw 
> data ) . I am intending to perform Segmntation ( watershed segmentation 
> and Region growing segmentation ). Right now, the application provided 
> for watershed segmentation operate on PGM(p2) format. Can you please 
> tell me what modifications do I need to apply on original program to 
> perform segmentation on my raw images ? )
> 
> Should I try converting my raw file into PGM format using program such 
> as GIMP ? What effect can it cause on original image ? Any information 
> on this if you have any will be appreciated.
> 
> Thanks,
> 
> Neha
> 

--------------090605030207070506070903
Content-Type: application/x-compressed;
 name="Watershed.tgz"
Content-Transfer-Encoding: base64
Content-Disposition: inline;
 filename="Watershed.tgz"
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--------------090605030207070506070903--